NEW: We changed the default behavior of save_tmp (now False). Pass --save_tmp for retrocompatibility
NEW: We changed the default beavior of save_panda_results. Now all PANDA outputs have column headers by default. Pass old_compatible for the previous behavior
Input data:
Expression: tcga_coad_cms2.nodot.txt
Motif data: /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt
PPI data: /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt
Start Panda run ...
Loading motif data ...
  Elapsed time: 2.90 sec.
Loading expression data ...
  Elapsed time: 0.43 sec.
Loading PPI data ...
Number of PPIs: 138479
  Elapsed time: 0.05 sec.
Calculating coexpression network ...
  Elapsed time: 4.33 sec.
Creating motif network ...
  Elapsed time: 3.66 sec.
Creating PPI network ...
  Elapsed time: 0.11 sec.
intersection /home/ubuntu/tcga-coad-subtype/priors/MotifPriorGencode_p5.txt tcga_coad_cms2.nodot.txt /home/ubuntu/tcga-coad-subtype/priors/ppi_Gencode_p5.txt False False False
Normalizing networks ...
  Elapsed time: 24.52 sec.
Running PANDA algorithm ...
Computing panda on CPU
step: 0, hamming: 3.729597296204977
step: 1, hamming: 0.7592292921269722
step: 2, hamming: 0.6138849810452524
step: 3, hamming: 0.5520854865801872
step: 4, hamming: 0.5047868017212607
step: 5, hamming: 0.46038229450461265
step: 6, hamming: 0.4166332113389577
step: 7, hamming: 0.37365584572196453
step: 8, hamming: 0.3321502879784829
step: 9, hamming: 0.29283734623003277
step: 10, hamming: 0.2562699608702944
step: 11, hamming: 0.22279244423519495
step: 12, hamming: 0.1925584504516589
step: 13, hamming: 0.16556805488775417
step: 14, hamming: 0.14170937073584663
step: 15, hamming: 0.1207955759950997
step: 16, hamming: 0.10259497213192657
step: 17, hamming: 0.08685393356918757
step: 18, hamming: 0.0733135808251009
step: 19, hamming: 0.06172130104002649
step: 20, hamming: 0.05183814676576758
step: 21, hamming: 0.04344325066406173
step: 22, hamming: 0.03633600445599319
step: 23, hamming: 0.03033668855591203
step: 24, hamming: 0.02528608016905273
step: 25, hamming: 0.021044409823688333
step: 26, hamming: 0.017489918134150084
step: 27, hamming: 0.014517223977125073
step: 28, hamming: 0.012035632807264393
step: 29, hamming: 0.009967468600739528
step: 30, hamming: 0.008246490896739235
step: 31, hamming: 0.006816425324485747
step: 32, hamming: 0.005629625872295411
step: 33, hamming: 0.00464587477284084
step: 34, hamming: 0.003831317208417759
step: 35, hamming: 0.003157525393820706
step: 36, hamming: 0.0026006823106871917
step: 37, hamming: 0.0021408748596345997
step: 38, hamming: 0.0017614849948265725
step: 39, hamming: 0.0014486681731792402
step: 40, hamming: 0.0011909084330808286
step: 41, hamming: 0.000978640376767604
Running panda took: 701.34 seconds!
Saving PANDA network to panda_tcga_coad_cms2.txt ...
WARNING: panda is now saved with the column names. 
Use old_compatible=True to save the panda results as previous versions without header
  Elapsed time: 45.37 sec.
